Recent developments in text mining research, and in scientific publication, have brought us to the moment when the long-standing potential of natural language processing technology to benefit biomedical researchers may finally be realized. Technological advances, recent results in computational linguistics, maturation of biomedical ontology, and the advent of resources such as PubMedCentral have set the stage for an attempt at an integrated computational analysis of a large proportion of the full text biomedical literature. Such an analysis has the potential to dramatically extend the way that biomedical researchers can effectively use the scientific literature, particularly in the analysis of genome-scale datasets, broadly accelerating and increasing the efficiency of scientific discovery. We hypothesize that it is now possible to extract a wide variety of ontologically-grounded entities and relationships by processing the entire PubMedCentral document collection accurately and with good coverage, to use this extracted information to produce new genres of scientifically valuable tools and analysis techniques, and to demonstrate its utility in the analysis of genome-scale data. The challenges that we plan to overcome range from fundamental linguistic issues (e.g. cross- document coreference resolution) to high-performance computing (e.g. scaling up integrated processing to include millions of complex documents), to fielding practical systems that can exploit enormous knowledge-bases to accelerate the analysis of very large molecular data sets.